It looks like some transactions got rolled back, probably because
there wasn't a recent enough checkpoint and the logs for the latest
transactions didn't get flushed to disk. Setting a more frequent
checkpoint interval would probably help.

How could I set this checkpoints?

You could read the slapd-bdb(5) manpage.

After setting checkpoint in my DB_CONFIG, the Server failed to start
with the following error. Rebuild and db_rocover shows the same error.